Base-by-base ratcheting of DNA/RNA in a Y-shaped nanochannel

ABSTRACT

A mechanism is provided for ratcheting a double strand molecule. The double strand molecule is driven into a Y-channel of a membrane by a first voltage pulse. The Y-channel includes a stem and branches, and the branches are connected to the stem at a junction. The double strand molecule is slowed at the junction of the Y-channel based on the first voltage pulse being weaker than a force required to break a base pair of the double strand molecule. The double strand molecule is split into a first single strand and a second single strand by driving the double strand molecule into the junction of the Y-channel at a second voltage pulse.

DOMESTIC PRIORITY

The present application is a divisional of U.S. patent application Ser.No. 13/971,486, filed Aug. 20, 2013, which is a continuation of U.S.patent application Ser. No. 13/724,041, filed on Dec. 21, 2012, thecontents of each application are incorporated by reference herein.

BACKGROUND

The present invention relates to nanopore/nanochannel devices, and morespecifically, to capture and control of molecules innanopore/nanochannel devices.

Nanopore sequencing is a method for determining the order in whichnucleotides occur on a strand of deoxyribonucleic acid (DNA). A nanopore(also referred to a pore, nanochannel, hole, etc.) can be a small holein the order of several nanometers in internal diameter. The theorybehind nanopore sequencing is about what occurs when the nanopore issubmerged in a conducting fluid and an electric potential (voltage) isapplied across the nanopore. Under these conditions, a slight electriccurrent due to conduction of ions through the nanopore can be measured,and the amount of current is very sensitive to the size and shape of thenanopore. If single bases or strands of DNA pass (or part of the DNAmolecule passes) through the nanopore, this can create a change in themagnitude of the current through the nanopore. Other electrical oroptical sensors can also be positioned around the nanopore so that DNAbases can be differentiated while the DNA passes through the nanopore.

The DNA can be driven through the nanopore by using various methods, sothat the DNA might eventually pass through the nanopore. The scale ofthe nanopore can have the effect that the DNA may be forced through thehole as a long string, one base at a time, like thread through the eyeof a needle. Recently, there has been growing interest in applyingnanopores as sensors for rapid analysis of biomolecules such asdeoxyribonucleic acid (DNA), ribonucleic acid (RNA), protein, etc.Special emphasis has been given to applications of nanopores for DNAsequencing, as this technology holds the promise to reduce the cost ofsequencing below $1000/human genome.

SUMMARY

According to an embodiment, a method for ratcheting a double strandmolecule is provided. The method includes driving the double strandmolecule into a Y-channel of a membrane by a first voltage pulse. TheY-channel includes a stem and branches, and the branches are connectedto the stem at a junction. The method includes slowing the double strandmolecule at the junction of the Y-channel based on the first voltagepulse being weaker than a force required to break a base pair of thedouble strand molecule, and splitting the double strand molecule into afirst single strand and a second single strand by driving the doublestrand molecule into the junction of the Y-channel at a second voltagepulse.

According to an embodiment, a system for ratcheting a double strandmolecule is provided. The system includes a membrane with a Y-channel,and the Y-channel includes a stem and branches, where the branches areconnected to the stem at a junction. The system includes a top fluidicchamber on one side of the membrane and a bottom fluidic chamber on anopposing side of the membrane. A first voltage pulse of a voltage sourcedrives the double strand molecule into the Y-channel of the membrane.The double strand molecule is slowed at the junction of the Y-channelbased on the first voltage pulse being weaker than a force required tobreak a base pair of the double strand molecule. A second voltage pulseof the voltage source drives the double strand molecule into thejunction of the Y-channel to split the double strand molecule into afirst single strand and a second single strand.

Additional features and advantages are realized through the techniquesof the present invention. Other embodiments and aspects of the inventionare described in detail herein and are considered a part of the claimedinvention. For a better understanding of the invention with theadvantages and the features, refer to the description and to thedrawings.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

The subject matter which is regarded as the invention is particularlypointed out and distinctly claimed in the claims at the conclusion ofthe specification. The forgoing and other features, and advantages ofthe invention are apparent from the following detailed description takenin conjunction with the accompanying drawings in which:

FIG. 1 is a cross-sectional view of a DNA-ratcheting nanodeviceaccording to an embodiment.

FIG. 2 is an abbreviated version of the nanodevice in which a membraneincludes two Y-channels according to an embodiment.

FIG. 3 illustrates a time-dependent biasing electric field chart toratchet a DNA molecule through the Y-channel according to an embodiment.

FIG. 4 is an abbreviated version of the nanodevice with sensors in theleft and right branches to respectively sequence single strand DNAmolecules according to an embodiment.

FIG. 5 is a method of ratcheting a double strand molecule through aY-channel according to an embodiment.

FIG. 6 is an abbreviated version of the nanodevice in which the membranehas Y-channels with multiple branches according to an embodiment.

FIG. 7 is a block diagram that illustrates an example of a computer(computer test setup) having capabilities, which may be included inand/or combined with embodiments.

DETAILED DESCRIPTION

Sequencing DNA at an affordable cost has inspired many new DNAsequencing methods. However, one existing technical challenge is tocontrol the motion of DNA at a single-nucleotide resolution. Withoutsuch control, some nucleotides could be read multiple times while someothers could be missed during a sequencing process. Therefore, it isdesirable to have a device that can nucleotide-by-nucleotide (i.e.,base-by-base) ratchet DNA. Nature has built a small yet efficientDNA-ratcheting machine: DNA polymerase is a protein molecule whichcontrols a directional motion of DNA nucleotide-by-nucleotide. DNApolymerase is used in a sequencing technology based on an existingmethod. To mimic the ratcheting process by the DNA polymerase, aman-made DNA-ratcheting machine is provided herein using syntheticnanomaterials. According to an embodiment, a nanodevice has a Y-shapednanochannel (e.g., a Y-channel) to electrically drive a double-strandedDNA (dsDNA) into the stem channel, followed by electrically unzipping ofthe dsDNA and threading each single-stranded DNA (ssDNA) through abranch channel.

Now turning to the figures, FIG. 1 is a cross-sectional view of aDNA-ratcheting nanodevice 100 according to an embodiment. A Y-channel140 is embedded in a membrane 101, and the Y-channel 140 is a Y-shapednanochannel. A double strand DNA molecule (dsDNA) 110 is being driventhrough and unzipped in the Y-channel 140 as discussed further herein.The membrane 101 may be a solid state membrane, such as, e.g., SiO₂,Si₃N₄, and/or another insulating material. The membrane 101 may have athickness of 100 nm. Generally, a channel can be a nanopore through asolid membrane or a surface channel in a typical nanofluidic device(such as a lab-on-chip) as understood by one skilled in the art.

One kind of Y-channel 140 is the Y-shaped carbon nanotube (Y-CNT) asshown in FIG. 1. Several methods have been developed to fabricateY-shaped CNTs which have been designed to transfer and multiply chargesignals at molecular level (molecular signal transduction).

Further information regarding Y-shaped carbon nanotubes is discussed inthe following articles which are herein incorporated by reference:Papadopoulos C, Rakitin A, Li J, Vedeneev A S, Xu J M (2000) Electronictransport in Y-junction carbon nanotubes. Phys Rev Lett 85:3476. DeepakF L, Govindaraj A, Rao C N R (2001) Synthetic strategies for Y-junctioncarbon nanotubes. Chem Phys Lett 345:5-10. Tu Y, Xiu P, Wan R, Hu J,Zhou R H, and Fang H P (2009), Water-mediated signal multiplication withY-shaped carbon nanotubes, Proc. Natl. Acad. Sci. 106, 18120-18124.

In the DNA-ratcheting nanodevice 100, two fluidic chambers (cis. andtrans.) 130 and 135 are separated by the solid membrane 101 andconnected to one another by the Y-channel 140. The top fluidic chamber130, the bottom fluidic channel 135, and the Y-channel 140 are allfilled with an electrically conductive solution 145. The electricallyconductive solution 145 is an electrolyte solution as understand by oneskilled in the art.

The Y-channel 140 (Y-CNT) has a stem 170 connected to left branch 172and right branch 174. FIG. 2 illustrates an abbreviated version of thenanodevice 100 in which the membrane 101 includes two Y-channels 140. Itis noted that multiple Y-channels 140 may be formed in the membrane 101.

Although understood to be present, FIG. 2 shows the nanodevice 100without the double strand DNA molecule 110 and the fluidic chambers 130and 135 so as not to obscure the figure. Example dimensions of theY-channel 140 are provided below. The stem 170 may have a width 205(and/or diameter) of 4 to 10 nm (nanometers) and/or sub ten nanometers.The left branch 172 may have a width 210 (and/or diameter) of 2 to 4 nmand/or sub 5 nanometers. The right branch 174 may have a width 212(and/or diameter) of 2 to 4 nm and/or sub 5 nanometers. The angle 250 ofa junction 220 may be 30 to 120 degrees, to form the left and rightbranches 172 and 174.

With reference to FIG. 1, a voltage source 106 is connected to electrode108 a in the top fluidic chamber 130 and connected to electrode 108 b inthe bottom fluidic chamber 135. The voltage source 106 (along withammeters 160 and 165 in FIG. 4) may be implemented in and/or controlledby a computer test setup 700 discussed in FIG. 7. Voltage pulse V₀ ofthe voltage source 106 is applied to the electrodes 108 a and 108 bwhich results in a biasing electric field E₀ being applied across themembrane 101, by inserting the two electrodes 108 a and 108 b into cis.and trans. chambers, respectively. The electrodes 108 a and 108 b may beAg/AgCl electrodes connected to a battery or any direct current voltagesource (e.g., the voltage source 106).

The (negatively charged) dsDNA molecule 110 can be electrophoreticallydriven into the stem 170 of the solid-state Y-channel 140 by the voltagepulse V₀ applied by the voltage source 106. When the dsDNA molecule 110arrives at the junction 220 (shown in FIG. 2) of the Y-channel 140, ahigher biasing electric field E₁ (i.e., a higher voltage pulse V₁ isapplied by the voltage source 106) is utilized to overcome the energybarrier for unzipping one base-pair of the dsDNA molecule 110, forbreaking two base-stacking, and for rotating the dsDNA segment by 36degree (the angle between neighboring base-pairs in dsDNA).Particularly, the higher voltage pulse V₁ (resulting in the higherelectric field E₁) breaks the dsDNA molecule 110 into ssDNA 112 in theleft branch 172 and into ssDNA 114 in the right branch 174 of theY-channel 140, when the dsDNA molecule 110 is driven (forced) into thesharp end of the junction 220.

Accordingly, once the dsDNA molecule 110 is driven through the stem 170to the junction 220 by the electric field E₀ (via the voltage pulse V₀),the dsDNA molecule 110 (temporarily) stops (or slows) at the junction220. Then, the higher electric field E₁ (via the voltage pulse V₁) isapplied, which is strong enough to break (i.e., overcome the energybarrier for unzipping) the base pair of the dsDNA molecule 110 that ispositioned at (abuts) the junction 220. After the voltage pulse V₁ isapplied by the voltage source 106 while the dsDNA molecule 110 abuts thejunction 220, the dsDNA molecule 110 unzips (i.e., the base pair isbroken) into the ssDNA molecule 112 and ssDNA molecule 114 respectivelyin branches 172 and 174. The ssDNA molecule 112 has a chain of singlebases (connected by a DNA backbone), and the ssDNA molecule 114 has achain of single bases (connected by a DNA backbone), as understood byone skilled in the art.

FIG. 3 illustrates a time-dependent biasing electric field chart 300 toratchet the DNA molecule 110 through the Y-channel 140 according to anembodiment. The y-axis shows the electric field E, and the x-axis showsthe time T.

As discussed herein, driving voltage pulse V₀ is applied by the voltagesource 106 to drive (i.e., move) the dsDNA molecule 110 from the topfluidic chamber 130 into the Y-channel 140, though the stem 170, and tothe junction 220 (i.e., temporarily stopping at the junction 220 becausethe electric field E₀ is not strong enough to break the base pairabutting the tip of the junction 220). For example, the chart 300 showsthat the electric field E₀ (via driving voltage pulse V₀) is applied fortime T₀ through T₁. Then, the higher voltage pulse V₁ is applied fortime T₁ through T₂ resulting in higher electric field E₁, as shown inFIG. 3. Once the higher electric field E₁ breaks (i.e., unzips) the basepair that was previously positioned at the junction 220, the drivingvoltage pulse V₀ is again applied (for time T₂ through T₃) to drive(i.e., advance) the dsDNA molecule 110 to position (i.e., stop) the nextbase pair at the junction 220. The higher voltage pulse V₁ is againneeded (and applied via voltage source 106 for time T₃ through T₄) tobreak this next base pair now positioned at the junction 220. Thisprocess repeats to ratchet the dsDNA molecule 110 through the Y-channel140 one base (i.e., one nucleotide spacing) at a time, and results inthe dsDNA molecule 110 being unzipped into the ssDNA molecule 112 andssDNA molecule 114.

As shown in FIG. 3, a pulse with a higher electric field E₁ is appliedto open one base-pair and thread two complimentary nucleotides into twobranches respectively. By alternatingly applying the lower drivingvoltage pulse V₀ and the (base pair breaking) higher voltage pulse V₁,FIG. 1 shows how the two ssDNA strands 112 and 114 are in two branches172 and 174 of the Y-channel 140 and shows the remaining dsDNA molecule105 is in the stem 170 of the Y-channel 140. Each time the high voltagepulse V₁ is applied, the DNA molecule 110 moves forward by onenucleotide (i.e., by one base), and this is the nucleotide-by-nucleotideratcheting. Note that motion of ssDNA in a CNT can be frictionless.Therefore, each ssDNA 112 and 114 can be easily driven by an electricfield through the Y-CNT (140). It is noted that when turning off thebiasing electric field (i.e., turning off the voltage source 106),hybridizing of two complementary ssDNA molecules 112 and 114 occursresulting in reverse ratcheting. For example, the dsDNA molecule 110moves in reverse which is back into the top fluidic chamber 130, whenthe voltage source 106 is turned off, and the again forms base pairs.

As one example, the energy required to break the hydrogen bond betweenthe base pair of the dsDNA molecule 110 (at the junction 220) is about2-3 k_(B)T, where k_(B) is the Boltzmann constant and T is thetemperature.

An example driving voltage pulse V₀ to drive the dsDNA molecule 110through the Y-channel 140 may be 0.1 volt, which results in the electricfield E₀ and a downward driving force. The downward driving force (fromcis. to trans.) does not break/unzip the base pair. The higher breakingvoltage pulse V₁ may be 0.2 volts, applied for approximately 0.1 μs(micro-seconds).

When one (or both) of the ssDNA molecules 112 and 114 exits a channelbranch (e.g., respective branch 172 and/or 174) and enters the bottomfluidic chamber 135, a sensor (e.g., pair of electrodes 150 as onesensor and a pair of electrodes 155 as another sensor) built on thesolid surface of the membrane 101 and at the end of a channel branch(e.g., branches 172 and/or 174) can be used to detect/read each base inthe ssDNA molecule 112 and/or ssDNA molecule 114. FIG. 4 illustrates thenanodevice 100 with sensors in the left branch 172 and the right branch174 to respectively sequence the ssDNA molecule 112 and the ssDNAmolecule 114 according to an embodiment. FIG. 4 is one example of howthe single strands may be sequenced and other sequencing methods may beutilized to read bases of the single strands, as understood by oneskilled in the art.

For example, a sensor can consist of the pair of electrodes 150 in theleft branch 172, and when a DNA base is in the gap of these twoelectrodes 150, an ammeter 160 can measure the base-sensitive tunnelingcurrent when voltage of the voltage source 162 is applied. To increasethe reading accuracy and efficiency, the nanodevice 100 can be used tosequence two complementary ssDNA strands 112 and 114 simultaneously inthe DNA ratcheting machine 100, which is another benefit of the currentdesign. For example, the base between the pair of electrodes 150 (ormaybe the previous or subsequent base) may be complementary to the base(concurrently) between the pair of electrodes 155, and the complementarybases can be respectively sequenced via respective voltages sources 162and 167 and respective ammeters 160 and 165.

For example, while the voltage source 162 applies voltage to the pair ofelectrodes 150 and while the voltage source 167 applies voltage to thepair of electrodes 155, the ammeter 160 measures the tunneling currentthrough the base (of the ssDNA 112) in the gap between electrodes 150 inthe branch 172, and the ammeter 165 measures the tunneling currentthrough the complementary base (of the ssDNA 114) in the gap betweenelectrodes 155 in the branch 174. Accordingly, the two complementary DNAstrands 112 and 114 are simultaneously or near simultaneously sequencedwhile the dsDNA molecule 110 is being ratcheted as discussed herein.This helps to confirm the accuracy of the bases being read in FIG. 4because the respective bases in branches 172 and 174 should becomplementary.

Complementary is a property shared between two nucleic acid sequences,such that when they are aligned antiparallel to each other, thenucleotide bases at each position will be complementary. Two bases arecomplementary if they form base pairs. For DNA, adenine (A) basescomplement thymine (T) bases and vice versa; guanine (G) basescomplement cytosine (C) bases and vice versa. With RNA, it is the sameexcept that uracil is present in place of thymine, and therefore adenine(A) bases complement uracil (U) bases.

FIG. 5 is a method 500 for ratcheting a double strand molecule (e.g.,the dsDNA 110) through a Y-channel according to an embodiment. Referencecan be made to FIGS. 1-4, 6, and 7. Various example may be for DNA butequally apply to RNA

The voltage source 106 (e.g., computer test setup 700) is configured (orcontrolled) to drive the double strand molecule 110 into a Y-channel 140in a membrane 101 by a first voltage pulse (V₀) at block 505. TheY-channel 140 comprises the stem 170 and branches 172 and 174, and thebranches 172 and 174 connect to the stem at the junction 220.

The voltage source 106 (e.g., computer test setup 700) is configured (orcontrolled) to slow the double strand molecule 110 at the junction 220of the Y-channel 140 based on the first voltage pulse (V₀) being weakerthan the force required to break a base pair of the double strandmolecule 110 at block 510.

The voltage source 106 (e.g., computer test setup 700) is configured (orcontrolled) to split the double strand molecule 110 into the firstsingle strand 112 and the second single strand 114 by driving the doublestrand molecule 110 into the junction 220 of the Y-channel 140 at asecond voltage pulse (V₁) at block 515.

The method further includes sequencing the first single strand (e.g.,ssDNA 112) one (e.g., left branch 172) of the branches, and sequencingthe second single strand (ssDNA 114) in another one (e.g., right branch174) of the branches. Sequencing the first single strand in the one ofthe branches comprises reading one base in the first single strand, andsequencing the second single strand in the other one of the branchescomprises reading another base of the second single strand, where onebase (between the pair of electrodes 150) on the first single strand(ssDNA 112) is complimentary to the other base (between the pair ofelectrodes 155) on the second single strand.

The method further includes simultaneously sequencing complementarybases of the first single strand and the second single strandrespectively in the branches 172 and 174.

The membrane 101 can include a plurality of Y-channels 140 (and/orY-channels 340 in any combination), each having a stem and branches suchas shown in FIGS. 2 and 6. The Y-channel 140 (340) is a Y-shaped carbonnanotube.

The voltage source 106 is configured to (automatically,semi-automatically, and/or manually) alternatingly apply the firstvoltage pulse (V₀) for a first time period (e.g., time T₀ through T₁)and the second voltage pulse (V₁) for a second time period (e.g., timeT₁ through T₂) until the double strand molecule 110 has been completelysplit into the first single strand (ssDNA 112) and the second singlestrand (ssDNA 114). The direction of the double strand molecule can bereversed (i.e., going from bottom fluidic chamber 135 to top fluidicchamber 130 (trans. to cis.)) through the membrane 101 by discontinuing(both) the first voltage pulse and the second voltage pulse applied bythe voltage source 106.

FIG. 6 is an abbreviated version of the nanodevice 100 in which themembrane 101 comprises Y-channels 340 with multiple branches accordingto an embodiment. The Y-channel 340 has stem 350 a main left branch 351and a main right branch 352. The main left branch 351 splits into asecondary left branch 353 and a secondary right branch 354. Similarly,the main right branch 352 splits into a secondary left branch 355 and asecondary right branch 356.

The following are example dimensions of the Y-channel 340. The stem 350may have a width 305 (and/or diameter) of 5 nm. The main left branch 351and the main right branch 352 may each have a width 310 (and/ordiameter) of 3.2 nm.

The secondary left branch 353 and the secondary left branch 355 may eachhave a width 315 (and/or diameter) of 2 nm.

The secondary right branch 354 and the secondary right branch 356 mayeach have a width 320 (and/or diameter) of 2 nm.

Although not shown so as not to obscure the figure, the branches 353,354, 355, and 356 may each have its own sensor (i.e., electrode pairconnected to a voltage source and ammeter) for reading the single bases.

As the stem 350 of Y-channels 340 is made large enough for dsDNA 110 toget in, the dsDNA 110 may go through either main left branch 351 or mainright branch 352. If the dsDNA 110 enters main left branch 351, theratcheting of dsDNA 110 occurs at the junction of the channels for thesecondary left branch 353 and secondary right branch 354. Two DNAstrands will be unzipped, and a single strand enters secondary leftbranch 353 and the complementary single strand enters secondary rightbranch 354, respectively (as discussed above in FIGS. 1-5).

FIG. 7 illustrates an example of a computer 700 (e.g., as part of thecomputer test setup for testing and analysis) which may implement,control, and/or regulate the voltage of the voltage source 106, andmeasurements of the ammeters 160 and 165 as discussed herein.

Various methods, procedures, modules, flow diagrams, tools,applications, circuits, elements, and techniques discussed herein mayalso incorporate and/or utilize the capabilities of the computer 700.Moreover, capabilities of the computer 700 may be utilized to implementfeatures of exemplary embodiments discussed herein. One or more of thecapabilities of the computer 700 may be utilized to implement, toconnect to, and/or to support any element discussed herein (asunderstood by one skilled in the art) in FIGS. 1-6. For example, thecomputer 700 which may be any type of computing device and/or testequipment (including ammeters, voltage sources, connectors, etc.).Input/output device 770 (having proper software and hardware) ofcomputer 700 may include and/or be coupled to the nanodevices andstructures discussed herein via cables, plugs, wires, electrodes, patchclamps, etc. Also, the communication interface of the input/outputdevices 770 comprises hardware and software for communicating with,operatively connecting to, reading, and/or controlling voltage sources,ammeters, and current traces (e.g., magnitude and time duration ofcurrent), etc., as discussed herein. The user interfaces of theinput/output device 770 may include, e.g., a track ball, mouse, pointingdevice, keyboard, touch screen, etc., for interacting with the computer700, such as inputting information, making selections, independentlycontrolling different voltages sources, and/or displaying, viewing andrecording current traces for each base, molecule, biomolecules, etc.

Generally, in terms of hardware architecture, the computer 700 mayinclude one or more processors 710, computer readable storage memory720, and one or more input and/or output (I/O) devices 770 that arecommunicatively coupled via a local interface (not shown). The localinterface can be, for example but not limited to, one or more buses orother wired or wireless connections, as is known in the art. The localinterface may have additional elements, such as controllers, buffers(caches), drivers, repeaters, and receivers, to enable communications.Further, the local interface may include address, control, and/or dataconnections to enable appropriate communications among theaforementioned components.

The processor 710 is a hardware device for executing software that canbe stored in the memory 720. The processor 710 can be virtually anycustom made or commercially available processor, a central processingunit (CPU), a data signal processor (DSP), or an auxiliary processoramong several processors associated with the computer 700, and theprocessor 710 may be a semiconductor based microprocessor (in the formof a microchip) or a macroprocessor.

The computer readable memory 720 can include any one or combination ofvolatile memory elements (e.g., random access memory (RAM), such asdynamic random access memory (DRAM), static random access memory (SRAM),etc.) and nonvolatile memory elements (e.g., ROM, erasable programmableread only memory (EPROM), electronically erasable programmable read onlymemory (EEPROM), programmable read only memory (PROM), tape, compactdisc read only memory (CD-ROM), disk, diskette, cartridge, cassette orthe like, etc.). Moreover, the memory 720 may incorporate electronic,magnetic, optical, and/or other types of storage media. Note that thememory 720 can have a distributed architecture, where various componentsare situated remote from one another, but can be accessed by theprocessor 710.

The software in the computer readable memory 720 may include one or moreseparate programs, each of which comprises an ordered listing ofexecutable instructions for implementing logical functions. The softwarein the memory 720 includes a suitable operating system (O/S) 750,compiler 740, source code 730, and one or more applications 760 of theexemplary embodiments. As illustrated, the application 760 comprisesnumerous functional components for implementing the features, processes,methods, functions, and operations of the exemplary embodiments.

The operating system 750 may control the execution of other computerprograms, and provides scheduling, input-output control, file and datamanagement, memory management, and communication control and relatedservices.

The application 760 may be a source program, executable program (objectcode), script, or any other entity comprising a set of instructions tobe performed. When a source program, then the program is usuallytranslated via a compiler (such as the compiler 740), assembler,interpreter, or the like, which may or may not be included within thememory 720, so as to operate properly in connection with the O/S 750.Furthermore, the application 760 can be written as (a) an objectoriented programming language, which has classes of data and methods, or(b) a procedure programming language, which has routines, subroutines,and/or functions.

The I/O devices 770 may include input devices (or peripherals) such as,for example but not limited to, a mouse, keyboard, scanner, microphone,camera, etc. Furthermore, the I/O devices 770 may also include outputdevices (or peripherals), for example but not limited to, a printer,display, etc. Finally, the I/O devices 770 may further include devicesthat communicate both inputs and outputs, for instance but not limitedto, a NIC or modulator/demodulator (for accessing remote devices, otherfiles, devices, systems, or a network), a radio frequency (RF) or othertransceiver, a telephonic interface, a bridge, a router, etc. The I/Odevices 770 also include components for communicating over variousnetworks, such as the Internet or an intranet. The I/O devices 770 maybe connected to and/or communicate with the processor 710 utilizingBluetooth connections and cables (via, e.g., Universal Serial Bus (USB)ports, serial ports, parallel ports, FireWire, HDMI (High-DefinitionMultimedia Interface), etc.).

In exemplary embodiments, where the application 760 is implemented inhardware, the application 760 can be implemented with any one or acombination of the following technologies, which are each well known inthe art: a discrete logic circuit(s) having logic gates for implementinglogic functions upon data signals, an application specific integratedcircuit (ASIC) having appropriate combinational logic gates, aprogrammable gate array(s) (PGA), a field programmable gate array(FPGA), etc.

The terminology used herein is for the purpose of describing particularembodiments only and is not intended to be limiting of the invention. Asused herein, the singular forms “a”, “an” and “the” are intended toinclude the plural forms as well, unless the context clearly indicatesotherwise. It will be further understood that the terms “comprises”and/or “comprising,” when used in this specification, specify thepresence of stated features, integers, steps, operations, elements,and/or components, but do not preclude the presence or addition of onemore other features, integers, steps, operations, element components,and/or groups thereof.

The corresponding structures, materials, acts, and equivalents of allmeans or step plus function elements in the claims below are intended toinclude any structure, material, or act for performing the function incombination with other claimed elements as specifically claimed. Thedescription of the present invention has been presented for purposes ofillustration and description, but is not intended to be exhaustive orlimited to the invention in the form disclosed. Many modifications andvariations will be apparent to those of ordinary skill in the artwithout departing from the scope and spirit of the invention. Theembodiment was chosen and described in order to best explain theprinciples of the invention and the practical application, and to enableothers of ordinary skill in the art to understand the invention forvarious embodiments with various modifications as are suited to theparticular use contemplated

The flow diagrams depicted herein are just one example. There may bemany variations to this diagram or the steps (or operations) describedtherein without departing from the spirit of the invention. Forinstance, the steps may be performed in a differing order or steps maybe added, deleted or modified. All of these variations are considered apart of the claimed invention.

While the preferred embodiment to the invention had been described, itwill be understood that those skilled in the art, both now and in thefuture, may make various improvements and enhancements which fall withinthe scope of the claims which follow. These claims should be construedto maintain the proper protection for the invention first described.

What is claimed is:
 1. A method for sequencing a double strand molecule,the method comprising: driving the double strand molecule into a firstY-channel and a second Y-channel of a membrane by a first voltage pulse,the first Y-channel includes a first stem and first branches, the firstbranches being connected to the first stem at a first junction; whereinthe second Y-channel includes a second stem and second branches formedin the membrane, the second branches being connected to the second stemat a second junction, wherein at least one of the second branches of thesecond Y-channel is connected to at least one of the first branches ofthe first Y-channel such that one or more of the first branches feedsinto the second Y-channel; slowing the double strand molecule at thefirst junction of the first Y-channel based on the first voltage pulsebeing weaker than a force required to break a base pair of the doublestrand molecule; splitting the double strand molecule into a firstsingle strand and a second single strand by driving the double strandmolecule into the first junction of the first Y-channel at a secondvoltage pulse; and sequencing the first single strand in one of thebranches and sequencing the second single strand in another one of thebranches.
 2. The method of claim 1, wherein sequencing the first singlestrand in the one of the branches comprises reading one base in thefirst single strand; and wherein sequencing the second single strand inthe another one of the branches comprises reading another base of thesecond single strand, the another base being complimentary to the onebase.
 3. The method of claim 1, wherein the double strand molecule isdeoxyribonucleic acid or ribonucleic acid.
 4. The method of claim 1,further comprising simultaneously sequencing complementary bases of thefirst single strand and the second single strand respectively in thebranches.
 5. The method of claim 1, wherein the membrane comprises threeor more Y-channels, each having a stem and corresponding branches. 6.The method of claim 1, wherein the Y-channel is a Y-shaped carbonnanotube.
 7. The method of claim 1, further comprising alternatinglyapplying the first voltage pulse for a first time period and the secondvoltage pulse for a second time period until the double strand moleculehas been completely split into the first single strand and the secondsingle strand.
 8. The method of claim 1, further comprising ratchetingthe double strand molecule by reversing a direction of the double strandmolecule through the membrane by discontinuing the first voltage pulseand the second voltage pulse.